The evolutionary history of histone H3 and CenH3 variants. A. The evolutionary history of 159 H3 and CenH3 variants was inferred using the Neighbor-Joining method . B. The evolutionary relationship of 128 non-redundant histone variants was inferred using the Neighbor-Joining method . Importantly, animal stem H3 variants are identical in a broad range of species: For example, H3.3A96 (1) is identical in Trichoplax, Hydra, Nematostella, Buddenbrockia, and identical H3.3S96 (2) is found in Drosophila, Strongylocentrotus, Branchiostoma, Xenopus and many mammals. Further, H3.1 (3) is identical in mammals from mouse to human. Identical H3.2 (4) variants occur in organisms like Trichoplax, Drosophila, Branchiostoma, Xenopus and many mammals. The monophyly of several eukaryotic clades was well supported by phylogenetic analyses of histone H3 variant sequences. Pairwise comparison of selected H3 variants (indicated by arrows) from Unikonta or Bikonta species, respectively, revealed very high degrees of sequence conservation resulting in only rough separation of these clades. Due to very limited sequence variability no support for chromista or plant monophlyly could be found. However, two ciliate classes, Oligohymenophorea (e.g. Tetrahymena and Paramecium) and Spirotrichea (e.g. Stylonychia and Euplotes) were faithfully separated. Importantly, multiple H3 variants from Eozoa (Excavata + Euglenozoa) branched close to conserved H3 variants from other groups, predominantly Chromalveolata (Euglena, Reclinomonas, Sawyeria, Trichomonas, Streblomastix). All long branching Eozoa (Leishmania, Trypanosoma, Diplonema, Giardia, Spironucleus) or Microsporidia (Enterocytozoon, Encephalitozoon) H3 variants are parasites.